Comparing output results from cellassign

In this notebook, we observe the annotation results obtained from cellassign https://github.com/Irrationone/cellassign Those results were obtained in R in the R markdown named: cellassign.Rmd/cellassign.html

In this exercice we first predict labels for the PBMC3k datasets using:

• the default signatures provided with cellassign (cellassign_dblabel)
• a small set of besca's signatures (bescaVvs)
• a larger set of besca's signatures, 2 versions (bescaMarkerF, bescaFv2)

PMBC3k predition by cellassign is compared with the sig-annot and auto-annot prediction.

import besca as bc
import scanpy as sc
import pandas as pd
import logging

sc.logging.print_versions()

WARNING: If you miss a compact list, please try `print_header`!
-----
anndata     0.7.5
scanpy      1.6.0
sinfo       0.3.1
-----
PIL                 8.1.0
anndata             0.7.5
annoy               NA
attr                20.3.0
backcall            0.2.0
bbknn               NA
besca               2.3+34.gf0f50cb
biothings_client    0.2.1
certifi             2020.12.05
cffi                1.14.4
chardet             3.0.4
colorama            0.4.4
cycler              0.10.0
cython_runtime      NA
dateutil            2.8.1
decorator           4.4.2
dominate            2.6.0
fbpca               NA
get_version         2.1
greenlet            0.4.17
h5py                2.10.0
idna                2.7
igraph              0.8.3
importlib_metadata  1.1.0
iniconfig           NA
intervaltree        NA
ipykernel           5.4.2
ipython_genutils    0.2.0
ipywidgets          7.6.2
jedi                0.18.0
jinja2              2.11.2
joblib              0.14.0
jsonschema          3.2.0
kiwisolver          1.3.1
legacy_api_wrap     1.2
leidenalg           0.8.3
llvmlite            0.35.0
lxml                4.6.2
markupsafe          1.1.1
matplotlib          3.3.3
more_itertools      8.6.0
mpl_toolkits        NA
mygene              3.1.0
natsort             6.2.0
nbformat            5.0.8
networkx            2.5
nose                1.3.7
numba               0.52.0
numexpr             2.7.2
numpy               1.19.5
packaging           20.8
pandas              1.2.0
parso               0.8.1
pexpect             4.8.0
pickleshare         0.7.5
pkg_resources       NA
plotly              4.14.1
pluggy              0.13.1
prometheus_client   NA
prompt_toolkit      3.0.9
ptyprocess          0.7.0
pvectorc            NA
py                  1.10.0
pycparser           2.20
pygments            2.7.3
pyparsing           2.4.7
pyrsistent          NA
pytest              6.2.1
pytz                2020.5
requests            2.19.1
requests_cache      0.5.2
retrying            NA
scanorama           1.7
scanpy              1.6.0
scipy               1.5.1
scvelo              0.2.2
seaborn             0.11.1
send2trash          NA
setuptools_scm      NA
sinfo               0.3.1
six                 1.15.0
sklearn             0.21.3
sortedcontainers    2.3.0
statsmodels         0.10.2
storemagic          NA
tables              3.6.1
terminado           0.9.2
texttable           1.6.3
tornado             6.1
traitlets           5.0.5
umap                0.3.10
urllib3             1.23
wcwidth             0.2.5
yaml                5.1.2
zipp                NA
zmq                 20.0.0
zope                NA
-----
IPython             7.19.0
jupyter_client      6.1.7
jupyter_core        4.7.0
notebook            6.1.6
-----
Python 3.7.1 | packaged by conda-forge | (default, Mar 13 2019, 12:57:14) [GCC 7.3.0]
Linux-3.10.0-693.11.6.el7.x86_64-x86_64-with-centos-7.4.1708-Core
24 logical CPU cores, x86_64
-----
Session information updated at 2021-01-06 17:32

PBMC prediction

We load the dataset predicted with Auto-Annot

pbmc3K_prediction = sc.read_h5ad("adata_predicted_16072020.h5ad")

In this pbm3k data are stored multiples scores and information. Leiden is the leiden clustering on the whole datasets post classical filtering. dblabel is the results of the sig-annot procedure on the whole dataset also after reclustering around T-cells/NK-cells for a finer grain annotation. Finally auto_annot is the results of the auto-annot procedure using Granja and Kotliarov datasets as training sets.

sc.pl.umap(pbmc3K_prediction, color = ["leiden", "dblabel", "auto_annot"], ncols = 1)

#bc.tl.auto_annot.report(pbmc3K_prediction, celltype = 'dblabel', method = 'autoannot', analysis_name= 'autoannot',
#                       train_datasets='pmbc3k',  test_dataset='GranjaAndKV', merge = True, use_raw=False)

Cellassign prediction

We load the prediction obtained with cellassign and upload the said results in our h5ad object.

cellassign predictions were obtained in R, please see cellassign.html / cellassign.Rmd

read_bescaF_prediction= pd.read_csv("pbmc3k_filtered_cellassign_bescaMarkersF.csv", header= None)
read_bescaF_prediction.index=list(read_bescaF_prediction[0])
read_bescaF_prediction=read_bescaF_prediction.drop(columns=0)
read_bescaF_prediction.rename(columns={1: 'bescaF_label'},
                 inplace=True)

read_bescaFv2_prediction= pd.read_csv("pbmc3k_filtered_cellassign_bescaFv2.csv", header= None)
read_bescaFv2_prediction.index=list(read_bescaFv2_prediction[0])
read_bescaFv2_prediction=read_bescaFv2_prediction.drop(columns=0)
read_bescaFv2_prediction.rename(columns={1: 'bescaF_label'},
                 inplace=True)

read_bescaVvs_prediction= pd.read_csv("pbmc3k_filtered_cellassign_bescaVvshort.csv", header= None)
read_bescaVvs_prediction.index=list(read_bescaVvs_prediction[0])
read_bescaVvs_prediction=read_bescaVvs_prediction.drop(columns=0)
read_bescaVvs_prediction.rename(columns={1: 'bescaF_label'},
                 inplace=True)


read_cellassign_prediction= pd.read_csv("pbmc3k_filtered_cellassign.csv", header= None)
read_cellassign_prediction.index=list(read_cellassign_prediction[0])
read_cellassign_prediction=read_cellassign_prediction.drop(columns=0)
read_cellassign_prediction.rename(columns={1: 'cellassign_label'},
                 inplace=True)

bescaF_probabilities=pd.read_csv("pbmc3k_filtered_cellassign_bescaMarkersF_probabilities.csv")
bescaFv2_probabilities=pd.read_csv("pbmc3k_filtered_cellassign_bescaMarkersF_probabilities.csv")
bescaVvs_probabilities=pd.read_csv("pbmc3k_filtered_cellassign_bescaVvshort_probabilities.csv")

Labels to dblabel

We need to map back the labels to dblabels using the dblabel nomenclature (described in besca in CellTypes_v1.tsv) when using the singlecell datasets provided by cellassign (in the celldex package)

set(read_cellassign_prediction['cellassign_label'])

{'B cells',
 'Cytotoxic T cells',
 'Epithelial cells',
 'Monocyte/Macrophage',
 'T cells',
 'Vascular smooth muscle cells',
 'unassigned'}

dblabel_mapping = {'B cells': 'B cell',
                            'Cytotoxic T cells': 'CD8-positive, alpha-beta cytotoxic T cell',
                            'Epithelial cells': 'epithelial cell',
                            'Monocyte/Macrophage': 'myeloid cell',
                            'T cells': 'T cell',
                            'Vascular smooth muscle cells': 'smooth muscle cell', 
                            'unassigned': 'unassigned'}

read_cellassign_prediction['dblabel_cellassign'] = read_cellassign_prediction.cellassign_label.copy().map(dblabel_mapping)

bescapath='/pstore/home/schwalip/src/bescapub/besca/'
### transform these short forms to dblabel - EFO standard nomenclature
nomenclature=pd.read_csv(bescapath+'/besca/datasets/nomenclature/CellTypes_v1.tsv',sep='\t',header=0,skiprows=range(1, 2))

read_bescaF_prediction["bescaF_label"].replace(to_replace='unassigned', value="Cell", inplace=True)
read_bescaF_prediction["bescaF_label"].replace(to_replace='Prolif', value="ProlifMyeloid", inplace=True)

read_bescaVvs_prediction["bescaF_label"].replace(to_replace='unassigned', value="Cell", inplace=True)
read_bescaVvs_prediction["bescaF_label"].replace(to_replace='Prolif', value="ProlifMyeloid", inplace=True)

read_bescaFv2_prediction["bescaF_label"].replace(to_replace='unassigned', value="Cell", inplace=True)
read_bescaFv2_prediction["bescaF_label"].replace(to_replace='Prolif', value="ProlifMyeloid", inplace=True)

read_bescaF_prediction["bescaF_label"]=[list(nomenclature.loc[nomenclature['short_dblabel']==x,'dblabel'])[0] for x in list(read_bescaF_prediction["bescaF_label"])]
read_bescaFv2_prediction["bescaF_label"]=[list(nomenclature.loc[nomenclature['short_dblabel']==x,'dblabel'])[0] for x in list(read_bescaFv2_prediction["bescaF_label"])]
read_bescaVvs_prediction["bescaF_label"]=[list(nomenclature.loc[nomenclature['short_dblabel']==x,'dblabel'])[0] for x in list(read_bescaVvs_prediction["bescaF_label"])]

read_bescaF_prediction["bescaF_label"].replace(to_replace='animal cell', value="unassigned", inplace=True)
read_bescaF_prediction["bescaF_label"].replace(to_replace='proliferating myeloid leukocyte', value="proliferating hematopoietic cell", inplace=True)

read_bescaFv2_prediction["bescaF_label"].replace(to_replace='animal cell', value="unassigned", inplace=True)
read_bescaFv2_prediction["bescaF_label"].replace(to_replace='proliferating myeloid leukocyte', value="proliferating hematopoietic cell", inplace=True)

read_bescaVvs_prediction["bescaF_label"].replace(to_replace='animal cell', value="unassigned", inplace=True)
read_bescaVvs_prediction["bescaF_label"].replace(to_replace='proliferating myeloid leukocyte', value="proliferating hematopoietic cell", inplace=True)

read_bescaVvs_prediction["bescaVvs_label"]=read_bescaVvs_prediction["bescaF_label"].copy()
read_bescaFv2_prediction["bescaFv2_label"]=read_bescaFv2_prediction["bescaF_label"].copy()

obs_bis = pbmc3K_prediction.obs.join(read_bescaF_prediction["bescaF_label"], how = "left")
obs_bis = obs_bis.join(read_bescaVvs_prediction["bescaVvs_label"], how = "left")
obs_bis = obs_bis.join(read_bescaFv2_prediction["bescaFv2_label"], how = "left")
obs_bis = obs_bis.join(read_cellassign_prediction["cellassign_label"], how = "left")
obs_bis = obs_bis.join(read_cellassign_prediction["dblabel_cellassign"], how = "left")

pbmc3K_prediction.obs  = obs_bis.copy()

for i in list(bescaF_probabilities.columns):
    pbmc3K_prediction.obs['P_'+i]=bescaF_probabilities[i]

    
for i in list(bescaVvs_probabilities.columns):
    pbmc3K_prediction.obs['PVvs_'+i]=bescaVvs_probabilities[i]

for i in list(bescaFv2_probabilities.columns):
    pbmc3K_prediction.obs['PFv2_'+i]=bescaFv2_probabilities[i]

sc.pl.umap(pbmc3K_prediction,color=['P_ClassMonocyte','P_cDC','P_pDC','P_CytotoxCD8Tcell','P_NaiTcell',
                                    'P_CD56dimNK','P_CD56brightNK','P_Mast'])

... storing 'bescaF_label' as categorical
... storing 'bescaVvs_label' as categorical
... storing 'bescaFv2_label' as categorical
... storing 'cellassign_label' as categorical
... storing 'dblabel_cellassign' as categorical

sc.pl.umap(pbmc3K_prediction,color=['PFv2_ClassMonocyte','PFv2_cDC','PFv2_pDC','PFv2_CytotoxCD8Tcell','PFv2_NaiTcell',
                                    'PFv2_CD56dimNK','PFv2_CD56brightNK','PFv2_NClassMonocyte'])

sc.pl.umap(pbmc3K_prediction,color=['PVvs_ClassMonocyte','PVvs_cDC','PVvs_pDC','PVvs_Bcell','PVvs_NKcell',
                                    'PVvs_Tcell','PVvs_NClassMonocyte'])

sc.pl.umap( pbmc3K_prediction, color = ["dblabel",'auto_annot' , 'bescaF_label','bescaFv2_label','bescaVvs_label',
                                        'cellassign_label','dblabel_cellassign'], ncols= 1)

#sc.pl.umap( pbmc3K_prediction, color = [ 'dblabel', "auto_annot", "KV_dblabel","Granja_dblabel","KVandGranja_dblabel" ], ncols= 2)

Comparing predictions

We fix the palette to keep the same colors for the UMAPs celltypes

values_ = set( pd.Categorical(pbmc3K_prediction.obs.dblabel).categories.tolist()+\
                  pd.Categorical(pbmc3K_prediction.obs.bescaF_label).categories.tolist()+\
                  pd.Categorical(pbmc3K_prediction.obs.bescaFv2_label).categories.tolist()+\
                  pd.Categorical(pbmc3K_prediction.obs.bescaVvs_label).categories.tolist()+\
                  pd.Categorical(pbmc3K_prediction.obs.dblabel_cellassign).categories.tolist()+\
                  pd.Categorical(pbmc3K_prediction.obs.auto_annot).categories.tolist())
import seaborn as sns 
#palette_ = sns.color_palette("tab10", len( values_) ) #
palette_ = sns.color_palette(n_colors=len( values_) ) #n_colors=30
palette_colors  = dict(zip(values_, palette_))
#palette_colors

bc.pl.update_qualitative_palette( pbmc3K_prediction, palette_colors,  group = 'dblabel', checkColors = True)
bc.pl.update_qualitative_palette( pbmc3K_prediction, palette_colors,  group = 'auto_annot', checkColors = True)
bc.pl.update_qualitative_palette( pbmc3K_prediction, palette_colors,  group = 'bescaF_label', checkColors = True)
bc.pl.update_qualitative_palette( pbmc3K_prediction, palette_colors,  group = 'bescaFv2_label', checkColors = True)
bc.pl.update_qualitative_palette( pbmc3K_prediction, palette_colors,  group = 'bescaVvs_label', checkColors = True)
bc.pl.update_qualitative_palette( pbmc3K_prediction, palette_colors,  group = 'dblabel_cellassign', checkColors = True)

sc.pl.umap( pbmc3K_prediction, color = ["leiden",  'dblabel'], ncols= 2)
sc.pl.umap( pbmc3K_prediction, color = ["leiden",  'auto_annot'], ncols= 2)
sc.pl.umap( pbmc3K_prediction, color = ["leiden",  'bescaF_label'], ncols= 2)
sc.pl.umap( pbmc3K_prediction, color = ["leiden",  'bescaFv2_label'], ncols= 2)
sc.pl.umap( pbmc3K_prediction, color = ["leiden",  'bescaVvs_label'], ncols= 2)
sc.pl.umap( pbmc3K_prediction, color = ["leiden",  'dblabel_cellassign'], ncols= 2)

Predictions reports generation

#annot_comparison in adata_pred.obs_keys()

adata_pred = pbmc3K_prediction
method = "cellassign"
merge = False
remove_nonshared  = True
use_raw = True
genes_to_use = ""
clustering = "leiden"
asymmetric_matrix= True

bescaF_label vs Sig-annot

fig = bc.tl.report(adata_pred, 
                   celltype =  "dblabel", method = "cellassign", 
                   analysis_name =  "bescaF",
             train_datasets= "bescaF", test_dataset= "pbmc3k", name_report= "cellassign",
             merge = merge, name_prediction = 'bescaF_label', 
             use_raw = use_raw,  genes_to_use = genes_to_use,
             remove_nonshared = False, clustering =clustering, asymmetric_matrix = True)

#fig.show()

WARNING: saving figure to file figures/umap.ondata_bescaF.png
WARNING: saving figure to file figures/umap.bescaF.png
Confusion matrix, without normalization
Normalized confusion matrix

bescaFv2_label vs Sig-annot

fig = bc.tl.report(adata_pred, 
                   celltype =  "dblabel", method = "cellassign", 
                   analysis_name =  "bescaFv2",
             train_datasets= "bescaFv2", test_dataset= "pbmc3k", name_report= "cellassign_Fv2",
             merge = merge, name_prediction = 'bescaFv2_label', 
             use_raw = use_raw,  genes_to_use = genes_to_use,
             remove_nonshared = False, clustering =clustering, asymmetric_matrix = True)

#fig.show()

WARNING: saving figure to file figures/umap.ondata_bescaFv2.png
WARNING: saving figure to file figures/umap.bescaFv2.png
Confusion matrix, without normalization
Normalized confusion matrix

bescaVvs_label vs Sig-annot

fig = bc.tl.report(adata_pred, 
                   celltype =  "dblabel", method = "cellassign", 
                   analysis_name =  "bescaVvs",
             train_datasets= "bescaVvs", test_dataset= "pbmc3k", name_report= "cellassign_Vvs",
             merge = merge, name_prediction = 'bescaVvs_label', 
             use_raw = use_raw,  genes_to_use = genes_to_use,
             remove_nonshared = False, clustering =clustering, asymmetric_matrix = True)

WARNING: saving figure to file figures/umap.ondata_bescaVvs.png
WARNING: saving figure to file figures/umap.bescaVvs.png
Confusion matrix, without normalization
Normalized confusion matrix

cellassign_label vs Sig-annot

fig = bc.tl.report(adata_pred, 
                   celltype =  "dblabel", method = "cellassign", 
                   analysis_name =  "cellassign",
             train_datasets= "cellassign", test_dataset= "pbmc3k", name_report= "cellassign_example",
             merge = merge, name_prediction = 'dblabel_cellassign', 
             use_raw = use_raw,  genes_to_use = genes_to_use,
             remove_nonshared = False, clustering =clustering, asymmetric_matrix = True)

WARNING: saving figure to file figures/umap.ondata_cellassign.png
WARNING: saving figure to file figures/umap.cellassign.png
Confusion matrix, without normalization
Normalized confusion matrix

Compare F1 Score

Besca report generate overall models. We retrieved the overall F1 and accuracy score for all reports generated in order to compare those values.

from os import listdir
from os.path import isfile, join
onlyfiles = [f for f in listdir(".") if isfile(join(".", f)) and '_report_' in f]

f1_values  = pd.DataFrame(columns=['accuracy', 'f1' ] , index=onlyfiles)

onlyfiles

['cellassign_Fv2_report_bescaFv2.csv',
 'cellassign_Vvs_report_bescaF.csv',
 'cellassign_Vvs_report_bescaVvs.csv',
 'cellassign_example_report_cellassign.csv',
 'cellassign_report_bescaF.csv']

for report in onlyfiles :
    get_info = open(report, "r").readlines()[3]
    dd = get_info.split(',')
    f1_values.loc[report] =[dd[1], dd[3].rstrip('\n')]
f1_values

	accuracy	f1
cellassign_Fv2_report_bescaFv2.csv	0.21845047923322683	0.2619440008400595
cellassign_Vvs_report_bescaF.csv	0.10982428115015974	0.1471481025732684
cellassign_Vvs_report_bescaVvs.csv	0.10982428115015974	0.1471481025732684
cellassign_example_report_cellassign.csv	0.05990415335463259	0.02819018981394475
cellassign_report_bescaF.csv	0.20247603833865815	0.2480235059887537

A large number of cells remain unassigned. In particular T cell assignment seems problematic.

END

! jupyter nbconvert --to html Cellassign_comparison.ipynb

[NbConvertApp] Converting notebook Cellassign_comparison.ipynb to html
[NbConvertApp] Writing 5425516 bytes to Cellassign_comparison.html

from sinfo import sinfo
sinfo()

-----
anndata     0.7.5
besca       2.3+34.gf0f50cb
pandas      1.2.0
plotly      4.14.1
scanpy      1.6.0
seaborn     0.11.1
sinfo       0.3.1
-----
IPython             7.19.0
jupyter_client      6.1.7
jupyter_core        4.7.0
notebook            6.1.6
-----
Python 3.7.1 | packaged by conda-forge | (default, Mar 13 2019, 12:57:14) [GCC 7.3.0]
Linux-3.10.0-693.11.6.el7.x86_64-x86_64-with-centos-7.4.1708-Core
24 logical CPU cores, x86_64
-----
Session information updated at 2021-01-06 17:30